Doctor Who: The Equestrian Chronicles, Season Two: The Fall
by Dr TimeKeeper
Summary: To be rebooted
1. Chapter 1

_Courier: ok guys this is a quick update. This series is taking its toll and I'm struggling to think of good ideas. So be patient and thank to the resent episode I have an idea that I can work with._

_Thank you for your patience_

Doctor Who:

The Equestrian Chronicles

S2 Ep01:

Parents Evening

It's been over 3 months since that Christmas and The Doctor has gotten used to life as father, The Tardis was now permanently set to just outside the library and a letter box was put up next to it, Scootaloo would come home every day from school with her friends and explore the vast interior of the time machine but this time she came back with a letter in her bag and after checking the control room and her father's lab she figured he would be next door.

**Golden oak Library**

"What! You mean to tell me you've been to the PAST and the FUTURE without me! You made a promise when we met that you'd teach me about time and space and now I hear you have taken two trips with two different ponies one of them being a child!" The Doctor was backing up from the angry Twilight with a sweat drop down the side of his head and her eyes blazing in fury.

"Well that time was an accident and you were busy at the gala not to mention the potential spoilers…" The Doctor explained which the truth was indeed for the most part.

"I'll have you know I was bored stiff and what spoilers you took Luna without a second thought" Twilight barked making the time lord fear for his current incarnation, Scootaloo who had overheard the conversation walked in to save The Doctors Skin.

"Hey Dad I have a letter for you" Scootaloo stated, giving the Doctor an excuse.

"Oh look Twilight parental duty calls, look I'll make it up to you I promise" after calming down Twilight sighed before returning to her job as a librarian "thanks Scoot, I owe you one" The Doctor whispered before taking the letter and opening it.

"No problem, maybe you can let me go to the field trip to Canterlot next week?" The Doctor looked up then down at his daughter in confusion.

"Field trip! Scoot I have a box that can go anywhere in time and space, why would you want to go on a field trip?" The Doctor said making Scootaloo think about it.

"Maybe so but when she goes on a field trip she will be with a teacher who will teach her about the area and different landmarks, it's supposed to be an educational experience" Twilight interjected with her vast bookworm knowledge with The Doctor looking at her for a moment processing.

"But that's boring!" The Doctor said to Twilight before turning back to Scootaloo "why would you want to go on a boring Education field trip with a teacher who probably doesn't even know what the word entertaining means" The Doctor then resumed reading the letter to which he immediately looked back to Twilight "Twilight can you go to Scootaloo's Parents evening" Twilight dropped her books before turning to the time lord in shock.

"You are unbelievable, you're the one who decided to adopt her and you're asking me to go to her parents evening in your place?" The Doctor thought carefully about his next words.

"Well if it was any other Teacher then i could endure it but I really can't stand that...what's her face?"

"Cheerilee, her name is Cheerilee" Twilight answered.

"That's it, she is very annoying, she keeps thinking I'm someone's boyfriend and I don't see the signs of that?" The Doctor continued.

"The term is Coltfriend and just tell her who you're really dating" Twilight added with a small smirk making The Doctor blush.

"And risk that level of gossip? No thanks plus its Luna who wants to keep it a secret not me" The Doctor covered his mouth with his hoof when he remembered who was in the room.

"You're dating the Princess!" Scootaloo yelled in surprise before The Doctor could cover her mouth.

"Scoot Sweetie, Daddies love life is a state Secret, so I need you to forget everything you just heard" getting irritated with her father's baby talk, she shoved his wing out of the way.

"Dad I'm not a baby, I can keep a secret" The Doctor stared at the orange filly with a raised eyebrow "What?"

"I barely trust you with knowledge of the Tardis, I can't have anyone outside this room knowing about this, not only will it cause the press to harass Luna but they will look for me and I don't like the attention" The Doctor explained

"Ok I won't tell anybody" Scootaloo replied before miming her mouth shut but The Doctor was not fooled.

"Not even your friend's, especially Sweetie Belle, if she told Rarity…oh Rassilon" Scootaloo made a cross over her heart signifying a promise "good, now we have that sorted I have to find a way out of this parents evening" The Doctor finished before walking out the door with Scootaloo.

"Good Luck with that" Twilight added as the door slammed shut "I keep telling him not to slam that door. He's going to break it"

**2 Weeks Later, Friday Night, Ponyville Elementary**

The Doctor had spent the entire fortnight trying to get out of his apparent duty to attend this event but in the end he was sat in the hallway with Scootaloo and the only thing that could contain his boredom was Apple Jack, Rarity was also in the room but The Doctor didn't want to get her talking.

"So how's the parental life treating ya?" Apple Jack asked.

"Good, never a dull moment apart from this. Do I have to do this every year?" The Doctor replied.

"Yup but don't worry Doc, it's not that bad. All you have to do is sit there and listen to what they have to say" Apple Jack added just as the door opened and button mash and his mother left with Miss Cheerilee sending them off, she then turned down the hall.

"Scootaloo" upon hearing the elementary teacher call out Scootaloo's name, the Time Lord groaned before standing up and walking into the class room with Scootaloo in tow. As The Doctor sat down Cheerilee froze at the sight of the nervous Doctor.

"You! You're Scootaloo's new parent I've heard so much about, what's it been? Half a year since we last met" Cheerilee said unimpressed "at least now you're willing to listen to what I have to say"

"Look we may have gotten off on the wrong hoof but last time you caught me off guard and to be honest…" what happened next was a blur to most as several ponies full clad in black combat uniforms barged into the classroom, one shot Miss Cheerilee and Scootaloo with a dart before placing a bag over The Doctors head, The Doctor tried to resist but before he could do anything he was hit across the face and fell unconscious. When he woke up the bag was gone but standing in front of him was a dark blue Pegasus with messy mane of a lighter shade of blue he wore a white t-shirt under a blue shirt with a colour identical to that of his mane, as The Doctor looked around he saw he was in a small room that was padded and no visible exit.

"Long time no see Doctor" the Pegasus greeted with an accent that was clearly American in origin.

"Ok three things, one thanks for getting me out of there, two I don't know who you are or what you want with me and three what happened to everyone at the school" The Doctor said keeping his dark brown eyes on this stallions calm blue eyes and The Doctor could see they were as old as his, was this pony a Time Lord?.

"You're welcome, that's not surprising and you'll find out soon plus your daughter has been returned to the golden oak library and everyone else's should be waking up around about know" The Doctor moved his legs expecting them to be bound but he was surprised that he was free to move.

"Why am I not bound?" The Doctor asked getting up.

"I trust you and even if you would try to do anything, you're not getting out of this room and I'm in now danger even if you kill me" the other Pegasus said calmly.

"What are you here as a hologram?" The Doctor added before poking the Pegasus making him raise an eyebrow.

"Do you seriously not know who I am?" the stallion asked leaning into The Doctor.

"Enlighten me?"

"Captain Jack Harkness, of the 51st century, we met in world war 2 during your ninth incarnation and again on your tenth, judging be your youth I'm guessing you on your twelfth" The Doctor gave this Harkness a shocked look, he mentioned world war 2 not world party 2, the Doctor still had no comments on that event.

"Well you've got the wrong Doctor but I am surprised I'm not the only person on this planet who's heard of a human" Jack Harkness sighed as he rubbed his face with his hoof.

"alright you can turn it off" upon his order the walls vanished leaving an open space in a large underground cavern, the Pegasus then walked passed the Doctor before looking back "I was hoping for the real deal not an imposter but you'll have to do"

"Hey! I'm no imposter, I've lived for over 300 years with that name in that Doctors honour during the Time war, I'm guessing you've heard of that since you know my old man in his ninth and tenth incarnation when I fought by his side he was honoured that his only son renamed himself after the man who never gave up and I've kept that promise since Gallifrey's destruction up to this day, so don't you dare call me an imposter again you got that fly boy!" The Doctor yelled making Harkness turn around.

"Is it wrong to say I'm turned on right now?" The Doctors anger was washed away by confusion and awkwardness.

"Ok whatever just tell me what you need me for?" The Doctor said trying to ignore Harkness's comment.

"There's been a murder, unicorn male in his late twenties" a young earth pony said from a desk up a small flight of stairs, all she had on was a pair of thin black glasses and a head set, she was a indigo coloured mare with a brown mane tied in a pony tail.

"So...what do you need me for?" The Doctor asked looking up then scanning around.

"Because this isn't the first and we're getting nowhere" Harkness answered putting on another headset.

"Well then I need pictures, data, clues everything!" The Doctor yelled trying to get an echo.

"How about a body?" a unicorn behind The Doctor spoke in a cold manner, he was a darker shade of grey than The Doctor and had pitch black hair with white highlights.

"If it hasn't been processed perfect, who are you two by the way?" The Doctor asked the two new additions.

"I'm Dr Greg Saddle" the Grey stallion answered before the mare spoke.

"Digit Binary…I know, my parents weren't very imaginative" after introductions were made Saddle lead The Doctor to the body.

**Unknown location, morgue**

Saddle was stood over a body covered by a white sheet however a blood patch had developed near the head, suggesting a blow to the head.

"Now I need to know are you squeamish?" Saddle enquired before attempting to lift the veil.

"Unless it involves pears I'll be fine" The Doctor assured before Saddle removed the sheet, lying before The Doctor was a young unicorn with a description identical to the one Binary provided but it was but a moment when The Doctor noticed something interesting.

"By Rassilon and Celestia with God on top, that's a bit barbaric" the unicorn was killed by a uncontrolled blood loss from removal of the horn.

"That's what I thought but have you noticed the Cutie mark?" Saddle noted and when The Doctor looked he could find one.

"Curious, so it's clear that whoever killed him wanted the horn but in doing so drained his magic pool…somehow" The Doctor grabbed a magnifying glass from the table and inspected the horn closer "I can see tool impressions, so we're looking for someone of this time and likely another Unicorn or Pegasus as an earth pony couldn't have used a tool like this effectively without being trained. Where was he found?"

"A back ally in central canterlot, as soon as the guard found him, the princess called us in after the third incident" The Doctor placed the Magnifying glass back and began to walkout.

"I'm assuming the lack of horn is what connects them so we're looking for a serial killer…oh and thanks for telling me where I am" Saddle's eye's widened after realising what he said.

**Main Hub**

"Ok Captain Harkness, I've had a look so now I need a map with point marked out of all murders since the first" Harkness smirked while Binary picked up a remote and brought the data the Time Lord needed on the wall.

"One step ahead of you" The Doctor gave Harkness a glance before scanning the city wide map.

"Who are you by the way?" The Doctor asked with the assumed leader of this little trio standing next to him not looking away.

"We're Torchwood; a top secret organization funded by the crown and founded by Starswirl the Bearded. We can take care of the planet but every now and again we need the best" The Doctor smiled as he recognised the name.

"Now I know where I've heard of you, you're that time agent who was in the centre of that whole children fiasco on Earth" The Doctor replied casually.

"Yea, it's been a good century for me since then" The Doctor could sense sadness in Harkness's voice but soon pulled his attention back to the map

"Ohh, whoever is doing this is good, there is not pattern between kills other than all the victims are Unicorns" The Doctor took a moment of silence before Binary broke it.

"Maybe their using their magic for power" the computer geek commented with both Pegasi turning towards her.

"Not bad, I made a similar deduction on the body, the cutie mark was gone and that mark symbolises the magic within one's self…" The Doctor turned back to the map and then pulled out his mobile "he wants us to know he's stealing magic, so I'm going to need my assistant" binary's eyes widened upon sight of the device.

"I thought Tick Tock searched him!?" Binary yelled as The Doctor dialled a number.

"Please…nobody ever searches the tie, who's Tick Tock? Never mind I'll find out later" The Doctor then began his conversation "hey Twi…yes I know…I'm fine by the way thanks for asking…look we can continue this another time, we've got a call and I need my partner…ok fine I'm take you travelling as soon as we're done…oh right I'm in canterlot I'll meet you on..." The Doctor took another look at the map "Joe's Donut store…cool see you and bring my bag" The Doctor finished his call and hung up"

"Is it wise to bring civilians into this?" Saddle added after overhearing the conversation.

"Best way for me to investigate without blowing your little secret, plus I work best with friends. By the way Jack I hope Celestia was told you were going to kid nap me?" Jack smiled before grabbing a long blue trench coat.

"Afraid it wasn't Celestia who called, these murders only happen at night so our orders came from Princess Luna, I'm guessing you know her" The Doctor put on his best poker face as these people couldn't know.

"We've met, stopped her from putting a ban on summer vacation" The Doctor answered without giving to much away and he moved towards the large vault door which seemed to be the exit with Jack close behind "guessing your coming too? Well I hope you're a good runner?"

"Oh you've know idea, Digit you've got the con" with a small salute from Binary both Jack and The Doctor left through the main entrance "how long will it take your friend to get here?" Jack asked as they ran to the surface.

"We've solved our share of mysteries and when I need her she's always there" reaching the top, the Doctor looked around and saw a hardware store with a ginger Unicorn with a ginger mane sitting by the counter.

"Jack is he supost to be up here" the unicorn asked in a cold manner but clearly alarmed.

"Don't worry Tick Tock he's agreed to help us" without a second glace The Doctor raced out the door with Jack right behind him.

"Where's Joe's from here?" The Doctor asked, Jack followed by bringing the leather strap on his leg up to his face which was revealed to be a cleverly disguised Vortex manipulator.

"South, 6 blocks" Jack spread his wings and began to hover earning a peculiar look from The Doctor "you've got wings too I might mention"

"Show off" the Doctor replied then burst out laughing before joining Jack in the Air "I can see why my old man likes you. Now Avanti!" on a word both ponies born in another universe speed off in order to save another bit by bit.

**Joe's Donut Shop**

In front of the familiar Donut shop Twilight appeared in a flash of pink light, she looked around for the Time Lord with his Tardis blue bag around her.

"Where is he?" unknown to her, behind her in the shadows another pair of eye fell on to her, her knowledge and ability to teleport from Ponyville to the capital proved a large supply of magical energy, as the owner of those eye's moved closer and closer he was halted by the arrival of an unknown face.

"Twilight there you are!" the grey Pegasus yelled landing in front of the purple unicorn but as soon as his hooves hit the ground he stopped then sniffed the air then carried on "you're 3.7 seconds late" The Doctor said before giving the prodigy student a hug.

"Shut up! And why are you hugging me" The Doctor was now looking down the alley behind her and could see a glimmer of light.

"Don't be alarmed but behind you there is a pony who was ready to kill you, now follow me into the shop slowly, like you don't know he's there" The Doctor whispered before breaking then being heart broken by the scared look on his best friends face but she complied and both walked into the donut shop "you ok?" The Doctor comforted, now back to his normal volume.

"You lured me here as bait didn't you?" Twilight got out beginning to tear up making The Doctor back up a bit.

"Maybe" The Doctor replied as Twilight shot him a glare of pure rage making him yelp and grab onto the nearest pony who happened to be Jack.

"Hello handsome" Jack greeted in a flirty manor before The Doctor leaped off and back at the fuming unicorn.

"In short yes, yes I did but I never assumed he would spot your arrival but likely he's gone. I was going to tell you beforehand I swear…and if it helps is official Royal business" Twilight took a deep breath before taking of The Doctors bag then throwing it at him.

"Next time tell me over the phone! You selfish excuse for a pony!" The Doctor put his bag on and bowed his head in disappointment in himself.

"I'm really sorry Twi" but in a split second he raised his head "but you're going to have too yell at me later, please may I introduce my current client Captain Jack Harkness" Jack then moved closer to Twilight picking up her hoof and kissing it.

"Hello there" with Jack's gesture Twilights anger faded as she blushed "I'll tell you that if he gets on your nerves I will be only a phone call away" Jack was then met with a blow to the head.

"Oi, there's a time and a place, we've got a murderer to catch" The Doctor then speed out of the building, Twilight giving a sigh soon followed with Jack rubbing the back of his head soon after.

**Torchwood**

Back at the hub all three of the ponies greeted Tick Tock as they descended into the secret super base.

"Twilight remember when you saw the Tardis?" The Doctor said as they descended the stairs.

"Yea, what about it?" Twilight added from behind both stallions.

"It's not as impressive" The Doctor said which seemed to offend Jack.

"Hey, at least mine doesn't look like an antique" Jack retorted before they reached the large vault door.

"Unlike my father's type 40, my type 45 actually chose it's appearance and she likes it, who am I to judge" The Doctor before Jack entered his passcode and opened the door.

"Twilight meet Dr Saddle and Binary, two of the most trustworthy ponies on the planet and also welcome to Torchwood" Jack introduced as she took in the massive interior of the structure.

"How did we get so far down?" The Doctor ran to the place he started and tapped the ground.

"Staircase is shorter on the inside! Work of Starswirl I bet. Hey jack what does this thing do exactly?" The Doctor yelled from the other end of the hub.

"It's a holo-box it projects a hard light room that can take the image of anything, from a wooden shack to the Royal throne chamber, the only thing it can't copy is the inside of your box" Binary explained before taking a drink of coffee.

"Of course not she would break your computers if she let you peak at the blue prints, could you bring up the scene of the last murder with a full interactive forensic HUD, Twilight need your book smarts" giving a sigh Twilight walked over to the Holo-box as Binary programmed it.

"Bring the box online…now" with a click a roof and walls appeared making the interior a white room but as a moment passed bits and pieces of the murder scene flew into place and a back ally was formed with a tone of bins and boxes along the edges.

"Cool, Binary please create a model of the victim" without a response the stallion lying in the morgue appeared on the ground "full detail" again with no response the stallion's wound began to bleed and his face glitched into the way it was found, Twilight gasped at the horror on his face and was comforted by a hoof on her shoulder "I'm sorry Twi if it's too much but I need you to know what I know"

"Ok what happened?" Twilight managed to let out before regaining her posture

"Right, well have you ever heard of Jack the Ripper?," The Doctor began.

"Yes I have the stallion that was never caught but he lived over 300 years ago" Twilight answered.

"Yes well like good Old Jack, the killer had an MO, removal of the horn from the base of the skull which would make the victim bleed out or if they somehow survived permanently brain damaged preventing identification through investigation but I noticed that the victim had now cutie mark"

"How is that possible?" Twilight added making her friend smile.

"Jack I need the personnel file of every victim in front of me" from outside the box Jack picked up a headset placing it on his head.

"You got it" Binary got the message and got the file on the victims before sending them to the box.

"He reminds me of that Detective, what was his name?" Binary noted before trying to remember said ponies name.

"Yea but the princess asked us to get The Doc, if it was Celestia then no doubt she would get The Doctor involved and call him in if it became necessary" Jack explained "but I get the feeling their going to meet soon enough.

Back in the Holo-box the files appeared one by one, a total 7 in all.

"3 victims all with one thing in common can you see the detail Miss Sparkle" The Doctor only called Twilight that when he was playing with her and trying to make her think on his level, he calls it a test, she calls it a challenge. Then it hit her she recognised some of the faces from her childhood.

"They all went to the School for Gifted Unicorns!" that detail made Binary look into it herself, she was right.

"Exactly, I deduced that the killer was collecting magical energy from the victims and the best place to get that level of energy would be from an attendee of the best school in the country but the killer isn't working alone, he had access to the locations of every victim before the themselves decided to go, outside a restaurant, inside their homes and occasionally in the back alleyway" The Doctor added making Twilight look around the crime scene and she saw several spots that any pony could hide behind.

"But how can someone know when someone will go somewhere without a written schedule…unless!" Twilight realised making her friend smile with satisfaction.

"Exactly, the real master mind has access to future knowledge and technology and must have planned these killings in advance, which is why they knew where you where the moment you teleported but they didn't anticipate me" The Doctor finished ecstatic with the puzzle finally solved "bring down the box" as the Holo-box shut down The Doctor looked at Jack with a massive smile on his face "get a list of all Ponies who attended that school at the same time as Twilight, that are still living in canterlot" in an instant both Jack and Binary began searching for those individuals.

"Got them, putting them up" Binary said as six names appeared on the wall.

"Ok, Twilight who out of these would you consider near you're level" Twilight looked over each of the six unicorns and spotted an old friend.

"Him, he was in the top 5 of my class, he was the most natural at spell casting even compared to me" overhearing the young Unicorn Jack brought up said ponies file.

"His name is Comet Tail, graduated the school with top marks, he works at the Canterlot university as a scientist, working on combining magic with technology" The Doctor read the file on the wall before turning to Twilight.

"Twilight, I need you to got to him and tell him his life's in danger" Twilight thought about it for a moment with questions in her mind.

"Hold on why can't we both go?" The Doctor signed looking down for a moment then at Twilight.

"Whoever is killing ponies is clever, he leaves no evidence that anyone can trace and plans out his kills efficiently, also there is no guarantee that your old classmate is the next target but I doubt he will miss out the chance for two kills for one…In other words and as delicately as I can you need to lure the killer in" Twilight looked into The Doctors eyes and could see that he didn't like his plan but she trusted him, that's what best friends do after all.

"Doctor if you tell me you've got my back then I'll believe you, you don't need to fear what could happen and just focus on what you want to happen" The Doctor smiled at his friends wise word before Tick Tock came down the stairs with a letter.

"Captain, another has been found, same M.O." this made both The Doctor and Jack look at each other in worry.

"Where?" Jack asked as Tick Tock gave the letter to jack after he read it his looked down in disappointment "were too late, description matches" Twilight was thankful she wasn't very close to Comet as she didn't want to feel the pain of losing a close friend but she still felt bad that they couldn't get to him in time.

"Well then change of plans, we're now CSI: Canterlot" The Doctor followed his comment by putting on a pair of sunglasses "let's go"

**Home of Comet Tail**

The Doctor, Twilight, Jack and Saddle all stood over the corpse of the innocent unicorn, not only were he brutally killed in the same way as the others but his home was ransacked as well.

"Same C.O.D, death by blood loss from horn removal" Twilight left the room unable to take the odour while The Doctor looked down in shame but as Jack began to investigate the room a distinctive ringing could be heard catching The Doctors attention immediately.

"Yours I presume?" Saddle asked as the ringing sounded a lot like a phone.

"Not mine…it's coming from the body" deciding to take a closer look The Doctor found a mobile similar to his own but definitely not his or any of his friends but it was still ringing so after exchanging a look with Jack and Saddle he accepted the call and placed the device to his ear "hello" the voice that replied spoke with high class, suggesting he was from this area but the fact he had access to human technology was very interesting.

"_Hello Doctor, we speak at last, I trust you're familiar with my work"_

"Yea, brutal to say the least but why?"

"_Why do I need to explain myself to you? But you want answers and both long for a challenge so I'm going to give you one, if you beat it then you win but if you fail then lives will be lost but don't worry Time Lord, this series of killings have __come to an end but the culprit will do me one final act, but only you can find him in time but don't be tardy or time will crumble" _after giving The Doctor his challenge he hung up but the phone buzzed with a text message which read.

'_Keep the phone –M'_

"I'm guessing that was the killer, what did he say?" Jack asked just as Twilight entered the room.

"No it was his handler but the guy's a nutter, yet he knows who I am, he said _'that the culprit will do him one final act, yet I can only find him in time__'_" The ponies thought about it for a second but they were getting nowhere but the Doctor noticed a plate of breakfast with the paper next to it "odd, Saddle when was T.O.D.?"

"Late last night…I'd say 11, why?" Saddle answered as The Doctor picked up the paper.

"Well this paper is issued today, not to mention the full plate of breakfast" The Doctor said just as Twilight figured it out for herself.

"Why would he make breakfast in the middle of the night? Unless" Twilight said with a The Doctor raising his eye brow.

"Unless, it wasn't made by the victim but by the real master mind, M as he seems to have identified himself" The Doctor read the paper which had the new Town clock on the front page. Then it hit him "OH! Of course!, oh that's so obvious!"

"What is?" Jack asked after jumping at the Time Lords outburst.

"He was being literal, you can only find him in time and the Canterlot Clock tower is being opened today" The Doctors explanation made everyone look at each other "It's a bomb if we don't stop him then the tower will crumble" Jack immediately contacted Binary while The Doctor ran out of the house with Twilight close behind.

"Doctor go on ahead, I'll catch up" The Doctor glanced back with a worried look.

"I'm not leaving you behind!" The Doctor yelled but his companion was not having it.

"Doctor Princess Celestia will be there, you need to get their as soon as possible" hesitating for a moment The Doctor couldn't ignore that detail and launched into the sky "Good Luck!" after The Doctor had left Twilight slowed to a halt with Jack close behind her "do you think he will make it?"

"If he's anything like his father then no doubt"

**Canterlot Clock tower**

"Fillies and Gentlecolts, we gather here together to celebrate the renovated Clock Tower" Celestia began as she addressed the crowd that gather but a faint yet familiar voice rang through her ancient ears making her look to the skies and The Doctor was racing at sonic speed.

"Stop the celebrations!" The Doctor landed blowing a cloud of dust before approaching the Princess "Princess you have to get everyone away from here, I have reason to believe that a bomb has been planted inside by a serial killer" Celestia's eyes widened at the Time Lords claim as The Doctor would have no reason to lie and it was better to be safe than sorry.

"Very well. Everypony please remain calm and evacuate the area, Guards escort them away from the tower" after notifying the Princess The Doctor Ran into the Tower in order to apprehend the murderer. At the top the light shone through the glass clock face and in front of The Doctor was a single unicorn stallion with a blood stained black cloak.

"Hello, Doctor I trust you've come to stop the bomb but I'm afraid even I don't know how to deactivate it" The Unicorn said with a weak voice.

"Well the area is evacuated, nopony will be harmed" both killer and Doctor stared each other down.

"Not my problem, my job was to make sure this bomb goes off but your blood will be spilt by my knife" The killer took out a short blade and launched towards The Doctor, the killer was faster than The Doctor thought, as the blade cut his wing knocking him to the floor, he was then grabbed by the neck with the blade making contact with his throat "thought you were the fastest? well sorry to say but Speed magic is one of my specialties but I did expect more from you, Goodnight" The Doctor thought over every solution he could think of luckily he dropped the phone and had access to his Screwdriver.

"Hey do you know what happens to eardrums when introduce to supersonic sound?" The Doctor asked still struggling.

"No why?" The Killer answered giving The Doctor his opening.

"Just checking" The Doctor activated his screwdriver sending out a signal that made the phone ring, the sound made the Killer stumble back in pain, The Doctor knocked him out with a roundhouse kick "you just got you ass kicked by science" The Doctor then examined the bomb, it was far to complex for an equestrian design but The Doctor had no clue how to deactivate it, then the voice that called him before spoke from the bomb.

"_What a shame, looks like you won't be getting out of here in time, bye bye Doctor" _the screen on the bomb then began ticking from 10 and The Doctor began to panic.

"Oh crap"

**Outside**

Standing with her subject Celestia stared at the Clock Tower hopping that The Doctor could disarm the bomb in time but her hope was in vain as the clock face erupted in fire and the tower followed suit, acting on instinct Celestia ran toward the tower to see if The Doctor was still alive.

**Before the explosion**

Thinking on his hooves The Doctor grabbed the killer and made a run for the window and he was about to hit the glass just as the counter hit 1, The Doctors vison was engulfed in fire but from the force of the explosion he and the Killer where pushed forward into the courtyard both landing with a large thud. As The Doctors vison retuned to him he saw Celestia kneeling above him.

"Doctor are you alright?" her voice was muffled by the shock wave affecting The Doctors hearing.

"Yea, got blown up, it was great, you should add it to your things to do list" The Doctor managed to upright himself as the mass of civilians gathered to fill their curiosity along with Shining armour and royal guard reinforcement to protect the princess.

"Princess are you alright?" Shining asked the second he was within ear shot of the Equestrian monarch.

"I am fine Captain but I believe The Doctor has something for you" Shining armour turned his attention to the Time Lord as he walked towards the unicorn murderer lying on the ground.

"Shining armour, this stallion is under suspicion of Murder on 4 counts and with intent to assassinate the Princess, if you would be so kind as to arrest him" The Doctor said as he turned to face his friend's sibling.

"Sure thing Doc" Shining replied with a smile as he ordered his men to apprehend the suspect.

"What!?" The Doctor yelled rubbing his ear still unable to hear properly making both Celestia and Shining laugh but at that moment The Doctor felt the vibrations of the phone in his possession.

"_Congratulations, you beat my test, I'll yield defeated. Till the next time, Time Lord -M" _knowing he should be glad that he once again saved lives, The Doctor couldn't help but wonder who this _M_ was but his thought where drowned out by the mass of reporters that had arrived.

"Captain what has transpired?" one of the reporters asked, thankfully none had noticed The Doctor but Shining armour was about to change all that.

"A series of killings and an attempt on The Princesses life was just halted" many other questions were asked but only one was heard through the chaos.

"Who do we have to thank for this heroism?" The Doctor was about to sneak away but halted in his tracks after hearing his name.

"Ponyville's very own Detective" Shinning said pointing at the Grey Pegasus "The Doctor" with a burning desire to kill Shining The Doctor turned around with all of the cameras flashing him his face with the reporters turning their attention to him along with the wave of questions.

"How did you know that The Princess was in danger?" the same reporter asked, The Doctor was up for flying away but if ponies saw hope in him then what was the harm with being known maybe it would cure his boredom.

"When the evidence is clear you can know anything and all signs pointed to an attack on the clock tower, however if it wasn't for my colleges who for the time being shall remain nameless, I would have never known about this attack" the reporters continued with more questions but one which everyone wanted to know.

"Excuse me Detective but you were called The Doctor, Doctor Who exactly?" as this question was asked The Doctor spotted Jack and Twilight in the distance, this made him think, if he became a hero then he would have to give up any chance of a peaceful life, so after making his decision he gave his answer

"Good question, have fun with that" The Doctor said with a smile then using all the speed he had shot off into the sky and flew above the clouds, taking a deep breath The Doctor flew back to Ponyville in order to do something he should have done properly from the start.

**Ponyville Elementary, the next day**

As Miss Cheerilee began to prepare for her class she heard a knock on her door which turned out to be The Doctor.

"Hello, can I help you?" Cheerilee asked as The Doctor stepped into the room, she seemed to have forgotten what had happened the previous night but she clearly remembered the first time they met "You!

"Yes sorry to bother you, I'm Scootaloo's father, I wasn't able to attend last night due to…uh, work but I was hoping if you had time to tell me about how Scootaloo's been doing" Cheerilee set a chair in front of her desk before sitting at it.

"Not a problem, Mr…?" Cheerilee paused as she was unable to remember his name.

"Keeper, Time Keeper" for the next half an hour both The Doctor and Cheerilee discussed how Scootaloo's grade have improved since she was adopted and afterwards The Doctor made his way back to the library to relax as Twilight would want to talk with Celestia and Scootaloo would have went to school. Before opening the door he had notice it was unlocked which was odd considering that Twilight wouldn't miss something like this "whose in here!?" he announced looking around only to see a middle aged mare sitting on the couch drinking a cup of tea "you do realise you're drinking my friends tea right?" the mare placed the cup down and looked over to the much older stallion.

"very perceptive of you Doctor but I grew weary of waiting" the mare stood up and into the light revealing her features, she had a short brown mane and a pale white coat, her cutie mark was that of an open umbrella.

"Who are you?" the Doctor asked taking a closer step.

"I am Mycroft Hooves" The Doctor stopped connecting her name to the initial given to him earlier.

"You're _M?_" The Doctor asked suspiciously

"I'm afraid not, I can confirm that the pony who contacted you is a stallion, I come to you because his interest has shifted from my younger brother to you" Mycroft continued looking The Doctor straight in the eye.

"How can I trust you?" The Doctor queried unable to get any emotion form the mare.

"I work for her highness as an advisor, simply put in my brothers crud words I am the government and I know about your relationship with Princess Luna" The Doctor took a step back in defence but she opened the door looking back "don't worry, your business with her highness is between you and her but I hope you grow to trust us as you have in captain Harkness, good day Doctor" leaving the Time Lord alone The Doctor wondered how long this world will stay as it is before crumbling into chaos but at least he knew that _M _is a stallion but for Equestria to be safe _M _had to be stopped.

Next Time:

Nightmare


	2. Chapter 2: prologue

Courier: I thought I would upload this as it has relevance to the next Episode. But I have a important change I need to address.

The Doctor is the Doctor, as in the original and I've made him the 16th incarnation.

Reason for this is because I forget sometimes that I made him a different character and I think of brilliant plot ideas that work better if I just use the original character.

So to tie in with the story I'll be changing everything that mentions the difference between the characters and making it fit. Things like age and the entirety of the last episode but until it's done backstage the chapters will remain as they are and S2 EP2 will take this retcon onwards.

Thank you and enjoy the short

Doctor Who:

Equestrian Chronicles

**Episode 2: Prologue **

_**The Doctors Blossom**_

The Doctor had finally grown accustomed to not being alone, he actually enjoyed being a Dad, he recently helped out with a school play, using his technical genius he had set the stage to do just about everything the teacher wanted. After watching the finished production he was extremely proud and he had the perfect black mail material since Scootaloo was force to wear a frilly dress. But as The Doctor walked past his adoptive Daughters room, he noticed that it was open just a crack which he found odd as the doors are programmed to shut completely when left open. As he moved closer he peered in ever so slightly and his hearts dropped as he saw the orange filly sobbing on her bed.

"Scoot? Are you ok?" hearing her father's voice suddenly made the young Pegasus shoot up.

"Dad!" she said surprised but also with a sadden tone like she had used all the air in her lungs for crying "why are you here?"

"Door was left open; guess the old girl was worried" The Doctor said referring to his age old home "why are you crying anyway? You ran in so cheerful you almost made me drop a thermo coupling"

"It's those two snot nosed snobs, Silver Spoon and Diamond tiara"

"What those two brats whose name is precisely what there cutie mark is, I mean please! how is a silver spoon supposed to represent a talent, its completely unheard off" The Doctor ranted before remembering he was trying to comfort Scootaloo "so, What are they teasing you about this time?"

"Everything wrong with me" Scootaloo replied rather bluntly as The Doctor sat down beside her.

"Now hold on wait a minute, there is nothing wrong with you Scoot, why would you listen to people saying otherwise?" Scootaloo jumped off her bed and face her father with teary eyes.

"I can't Fly! And I'm almost 9 years old! Every Pegasus I know has learned to fly before their 9th birthday and I can barely keep off the ground. Not to mention the fact I still don't have my cutie mark!" The Doctor looked at his own wings and back at the crying filly.

"you know what? Come with me" The Doctor got up of the bed and urged Scootaloo to follow him.

After a couple minutes both Pegasi where standing in front of a door which after opening revealed a room Scootaloo had never seen before, it was the most beautiful garden she had ever seen, the grass bright green with trees covered with shining silver leaves, looking up the filly say the burnt orange sky and the twin suns setting in the distance.

"What is this place?" Scootaloo asked lifted a bit from her depression.

"This is my personal garden but unlike most gardens, I just let it get on with life, every plant in this room is the rarest plant on every planet I visited, the Tardis takes a sample of every form of plant life when I land and extract the information to create seeds but only the rarest are planted here" The Doctor explained walking along a metal plated path.

"Ok, why bring me here?" the filly followed her father until he stopped at a small flower bed.

"Because I wanted to show you this" what The Doctor was looking at was a bright white flower that had yet to bloom, taking a small water canister The Doctor gently sprayed the flower "this is a Schlenk Blossom, this flower is from my planet, Gallifrey and is considered the most beautiful flower in the cosmos, fetching high prices in intergalactic markets…but once my planet was destroyed this is one of the last surviving Schlenk Blossoms left. I'm just lucky it plants itself once it dies" both The Doctor and Scootaloo watched the flower as it ever so slightly reacted to the water. After a few minutes the small plant bloomed and it petals did something that shocked Scootaloo, the setting sun reflected off all the trees silver leaves and as soon as the light hit the blossom all the beams of light became different colours, one for every strip on Rainbow Dash's hair and some Scoot had never seen before. It was the most amazing thing she had seen on this box of miracles but she then noticed a powerful aroma coming from the flower, it was magnificent, she turned to see her father with his eyes closed just taking in the scent of his home.

"It's beautiful" she said softly as the Time Lord opened his old eyes.

"And do you know who this reminds me of?"

"Who?" Scootaloo replied cocking her head.

"You. You see Scoot you are currently like the blossom was before it bloomed, Bright and full of potential. Now if I had left it alone, it would take another several years to bloom because this plant is able to read the emotions and sentiment of those around it, therefore growing quicker if cared for and tended. Yes your cutie mark and ability to fly have not come yet but if you believe in your friends support and are just that little bit patient, on that day you will be as important and amazing as this little flower" Scootaloo's eyes widened and began to tear up once again but this time, tears of joy. After closing his eyes to relax and taking in the scent he was caught off guard by Scootaloo suddenly hugging him.

"Thank you Dad" The Doctor hesitated for a bit, as soon as Scootaloo left the orphanage, she had started calling The Doctor Dad instead of Doc, which he didn't mind but at this moment as he embraced his daughter in his arms that he truly felt worthy of having that title.

"You're welcome my little Blossom"


End file.
